A method for printing a three-dimensional part and a support structure with an electrophotography-based additive manufacturing system. The method includes developing a support layer of the support structure from a soluble support material with a first electrophotography engine, and transferring the developed support layer from the first electrophotography engine to a transfer medium. The method also includes developing a part layer of the three-dimensional part from an ABS part material with a second electrophotography engine, and transferring the developed part layer from the second electrophotography engine to the transfer medium. The method further includes moving the attracted part and support layers to a layer transfusion assembly with the transfer medium, and transfusing the moved part and support layers together to previously-printed layers with the layer transfusion assembly.